Articles tagged with Transcriptomics
Researchers at Nagoya University have identified giant-nucleus cells as precancerous markers in the kidneys, which emerge in response to iron toxicity and BRCA1 mutations. These cells exhibit cancer-related gene activity and can signal early cancer development in surrounding tissue, with distinct biological profiles in BRCA1-mutant rats.
Researchers have identified a hidden defect in the gut that can damage intestinal cells, even in patients with well-controlled disease. The study found that this defect can be present in patients with clinically mild disease and can lead to future flares.
A study finds that dementia with Lewy bodies preferentially affects certain brain regions, including those with genes linked to mitochondrial function and synapses. These regions show distinctive patterns of serotonin, dopamine, and GABA receptors, suggesting a potential target for new treatments.
Researchers from USC-led study found that different epigenetic clocks capture distinct aspects of cellular aging, while introducing new gene-expression based clocks with stronger predictive power. These tools can better predict age-related disease and mortality by examining DNA methylation patterns and gene expression.
A study found 161 differentially expressed genes in individuals with opioid dependence, including genes involved in immune and inflammatory processes. The researchers also developed a transcriptomic aging clock that predicts chronological age from gene expression patterns.
A new study uses spatial transcriptomics to map the molecular evolution of prostate cancer and identifies key genes associated with disease progression. The research reveals that genetic malignancy in specific glandular epithelial regions tightly aligns with increasing clinical Gleason scores.
Researchers at Vanderbilt University Medical Center used spatial transcriptomics to characterize acute rejection and response to immunomodulatory therapies following heart transplantation. The study linked cell-specific gene expression patterns to the development of cardiac allograft vasculopathy, a form of chronic rejection that limit...
A Northwestern University study found that viral reservoirs in a proxy animal model of HIV share features with immune-suppressive tumor microenvironments, suggesting that future HIV cure strategies may benefit from traditional cancer therapy approaches. By examining the broader tissue microenvironment, researchers identified shared bio...
Researchers discovered a strong link between environmental variation and thyroid hormone signaling in reef fish, enabling them to adapt to changing habitats. The study found that habitat impacts development by altering gene expression and metabolic profiles, giving animals more flexibility when their environments change.
The Human Cancer Model Initiative released a compendium of more than 150 organoid models of 25 types of cancer, which are now available to scientists worldwide. These patient-derived organoids provide state-of-the-art research tools for accelerating discovery and developing personalized treatment strategies.
Researchers identified a key enzyme, CtUGT52, that drives hydroxysafflor yellow A biosynthesis in safflower. The discovery enables breeders to select for medicinal safflower lines and paves the way for industrial production of flavonoid glycosides.
A new study by Sanford Burnham Prebys found that bolstering the SORLA protein can reduce tau tangle toxicity, a common culprit in Alzheimer's disease and other neurodegenerative disorders. This suggests potential as a therapeutic strategy for treating these conditions.
Researchers developed a new computational approach to identify genes that characterize different cellular states from mRNA-seq data, offering more accurate and interpretable analysis of complex biological data. The Cartesian Distance-Based Gene Expression (CDBGE) algorithm was evaluated using multiple publicly available datasets, demon...
A new study reveals that macrophages, a key immune cell type, age differently across tissues and between sexes. The researchers found that aging macrophages become more focused on responding to stress and cellular damage, but lose some molecular programs involved in maintaining healthy tissue structure.
A new study links tire pollution to Alzheimer's disease through the exposure to 6PPD-quinone, a chemical formed from shaved-off tire particles. The researchers used computational methods to identify key genes that predict Alzheimer's disease and found strong binding of 6PPD-quinone to these genes.
Researchers have identified 18 distinct cell type clusters in the inflorescence meristem that generate a plant's above-ground organs. The study provides new insights into how stem cells make the transition from an undifferentiated state to specialized cell types.
A study from the University of Oklahoma reveals that microplastic exposure can exacerbate fatty liver disease, especially in high-fat dietary conditions. Researchers used advanced mapping technology to pinpoint specific regions of liver damage caused by polyethylene exposure.
Researchers found that zirconia implants trigger an immune-inflammatory niche marked by macrophage involvement and COL6A2/CD44 signaling. In contrast, titanium implants support a regenerative microenvironment with collagenase-1/stromal-derived cell differentiation 1 (SDC1) signaling.
Researchers discovered a previously unknown enzyme system in anaerobic bacteria that converts toxic chloromethane into non-toxic substances. The system, found in species Acetobacterium dehalogenans, has implications for environmental remediation and climate research.
Researchers analyzed brain tissue from MSA patients and found that the immune cells known as microglia appear to be exhausted or dysfunctional in later stages of the disease. The study suggests that an overactive immune system may contribute to the development of MSA, providing a potential target for future treatment.
Researchers have developed a new system to map gene expression across whole mouse bodies, providing a toolkit for studying molecular and cellular processes. The technique allows for the analysis of inflammation in every cell type and organ tissue, paving the way for a 'virtual mouse' model that could be used for research.
Researchers find that rare stromal cells are responsible for maintaining immune cell organization in healthy lymph nodes. However, in aggressive lymphomas, this process breaks down due to a self-reinforcing inflammatory cycle, leading to tissue collapse and poorer outcomes.
Researchers at DZNE identified five particularly affected cell types in the motor cortex, which are equally susceptible to ALS and FTD. The study used molecular fingerprinting to analyze human tissue samples and found that excitatory cells are primarily affected by the disease.
New research reveals that tumor cells in supratentorial ependymomas cluster into distinct neighborhoods, each with a specific role, such as proliferating or invading. Understanding these cell subtypes could help predict treatment response and inform targeted therapies for this aggressive childhood brain cancer.
Researchers developed an integrative analysis of single-cell sequencing and spatial mapping to reveal novel mechanisms driving breast cancer metastasis. The study identifies key drivers of metastasis, including early disseminated cancer cells with enhanced invasive capabilities.
The development of spatial transcriptomics has advanced gene expression understanding, but selecting suitable analytical approaches is challenging. A database curated SpatialToolDB addresses this by classifying over 600 ST analytical tools and providing access to processed datasets.
Rice bioengineer Jerzy Szablowski has been awarded a Sloan Research Fellowship for his innovative work on noninvasive methods to communicate with the brain. He aims to develop versatile platform technologies to obtain new types of research data and treat multiple diseases.
A study by RIKEN researchers identifies a MYCN-driven biomarker that predicts the risk of liver cancer. The biomarker, known as the MYCN niche score, uses machine learning to analyze gene expression patterns and indicates whether a tumor-free liver is at high risk for developing tumors.
A new study found that shingles vaccination is associated with lower inflammation, slower epigenetic aging, and overall slower biological aging in older adults. Vaccination showed benefits even four years after the initial dose.
A new study maps the impact of stressors during pregnancy on the developing fetal brain, revealing a cell atlas and identifying key immune pathways. The research sheds light on how maternal gut-immune disruptions can shape neurodevelopmental disorders in children.
A deep learning framework called PRTS accurately predicts single-cell-resolution spatial transcriptomics from H&E-stained histology images. The model identifies 21 cell subtypes in mouse brain and maintains prediction accuracy in human breast and lung cancer tissues.
A recent study published in Cell Reports found that the vagus nerve's right branch is responsible for sensing nutritional information and reinforcing dietary behaviors. This research has implications for improving treatments of obesity, metabolic diseases, depression, and substance abuse.
Researchers at University of Texas M. D. Anderson Cancer Center discover that inflammation is responsible for driving the earliest stages of lung cancer, identifying potential targets for early intervention and suggesting a promising approach to intercepting lung cancer development.
Researchers created a comprehensive single-nucleus transcriptomic atlas of the pig intestine, identifying 19 major cell types and 58 cellular subtypes. This study provides valuable insights into the mechanisms by which neurons regulate inflammatory responses and the molecular basis for stronger immune functions in wild boars.
HTGAnalyzer is an automated tool simplifying complex transcriptomic workflows, enabling clinicians without bioinformatics expertise to perform essential analyses in precision medicine. The tool has been validated using multiple datasets and identified differentially expressed genes linked to cancer diagnosis, treatment, and prognosis.
Researchers developed TraMA, an RNA-based measure of biological aging that predicts health risks and mortality. It captures distinct aspects of aging and health decline, including inflammation, immune function, and kidney and brain health.
The Northwestern University-developed SOAR platform helps researchers understand diseases and find potential treatments by analyzing gene activity across various tissues. This tool enables prioritization of drugs to be sent to clinical studies, reducing development time.
Researchers at IGTP reveal a clear separation between lesional and non-lesional tissue, with high expression of pro-inflammatory genes in lesions. The study identifies 17 differential transcriptomic modules and associates molecular profiles with clinical indicators from the same patients.
Researchers at the University of Würzburg have developed a new, efficient method for recording gene activity in bacteria. The MATQ-seq protocol achieves a high cell retention rate of 95% and detects the activity of 300 to 600 genes per bacterial cell.
Researchers mapped a lung tumor's cellular neighborhoods in 3D using single-cell spatial technologies, identifying 18 cell types and potential targets for personalized cancer therapy. The study reveals new insights into how tumor cells interact with their surroundings and how to reverse immune suppression mechanisms.
Recent research reveals that avapritinib, a PDGFRA inhibitor, demonstrates potent activity against pediatric high-grade glioma tumors with PDGFRA alterations. Clinical trials in patients showed an initial clinical response and improved survival rates, suggesting the potential for avapritinib as a therapeutic option.
Researchers have developed a computational tool, Spotiphy, that uses generative AI to enhance the resolution of sequencing-based spatial transcriptomics without sacrificing gene coverage. This breakthrough enables single-cell resolution in tissue imaging while maintaining full transcriptome coverage.
A new technique called cycleHCR uses DNA barcodes to track hundreds of RNA and protein molecules in single cells within thick biological samples. This allows researchers to decipher how genes function in different parts of an organism, how they enable development, and how they might be altered in diseases.
A new Northwestern University study found that enhancing the brain's immune cells can clear Alzheimer's plaques and restore a healthier brain environment in immunized patient brains. The findings could reshape the future of Alzheimer's treatments by shifting the focus from removing plaques to harnessing the brain's natural defenses.
A new study finds that dexamethasone, a commonly prescribed anti-swelling drug, can significantly reduce the body's immune response to brain cancer for weeks after its last dose. This effect is stronger with higher dosages and may impact immunotherapy treatments.
A new method combines traditional histopathology with spatial transcriptomics data to improve understanding of chronic kidney disease lesions at the cellular and molecular levels. This approach has the potential to identify new biomarkers and therapeutic strategies for patients.
A new study combines genomic-scale microscopy with a technical innovation to capture genes bacteria turn on in different situations and environments. This technology promises to take the study of bacteria to the next level by providing powerful new insights into bacterial behavior, including gene expression and interactions.
Researchers at La Jolla Institute for Immunology discovered that tissue-resident memory CD8 T cells rise up to fight infections in the small intestine, using spatial transcriptomics technology. These immune cells are split between villi and crypts, with progenitor-like cells replenishing effector T cells.
A zebrafish protein, Hmga1, has been found to unlock dormant genes for heart repair in mice. The discovery could lead to regenerative therapies to prevent heart failure in humans.
Scientists at the Allen Institute have identified specific cell types in the brain that undergo major changes with age, which could lead to new treatments for age-related brain diseases. The study provides a detailed map of brain cells affected by aging and highlights potential connections between diet, inflammation, and brain health.
Researchers found that neural stem cells have a rejuvenating effect on nearby brain cells, while T cells promote stress and damage. The study opens new avenues for research into slowing or reversing brain aging.
The InSTAnT Toolkit allows scientists to investigate cellular processes by identifying proximal pairs of RNA transcripts, revealing sets of molecules that work together. This technology provides accurate and reproducible findings, shedding light on the complex interactions within cells.
Ewing sarcoma, a rare childhood cancer, is made more aggressive by the absence of STAG2 protein. This discovery provides potential biomarkers and therapeutic targets for treatment.
Researchers found that genetic collisions between transcription and DNA replication lead to large tandem duplications in cancer cells, which can be identified through dosage imbalance. These duplicates are associated with poor patient survival and high correlation with mutations in genes TP53, CDK12, and SPOP.
Researchers have identified a genetic signature that can predict neonatal sepsis in newborns before symptoms appear, allowing for earlier recognition and life-saving treatment. The discovery has the potential to improve healthcare outcomes in lower- and middle-income countries where neonatal sepsis is most prevalent.
Researchers have created a comprehensive atlas of zebrafish development, combining time-lapse videos and gene expression data to map the behavior of individual cells. This breakthrough tool offers new insights into how lifeforms develop from single cells to complex organisms.
A new study by Bar-Ilan University researchers found a significant link between the gut microbiome and aggression in mice, with reduced diversity in gut bacteria causing increased aggression. The study also identified key brain regions and biochemical mechanisms underlying these behavioral changes.
Researchers discovered faulty immune processes responsible for lingering lung issues after COVID-19, which can be disrupted by existing drugs. The study also identified molecules responsible for the issue and potential therapeutic options for patients with ongoing lung damage.
Scientists have mapped the global repertoire of genes that determine the male or female sexual fates in Plasmodium falciparum malaria parasites. This study reveals key regulators of gene expression during development and identifies novel candidate 'driver' genes, shedding light on the complex biology of malaria transmission.
Researchers have created the first spatial map of malaria infection in the mouse liver using Spatial Transcriptomics and single-cell RNA-sequencing. This discovery sheds light on the parasite's lifecycle, revealing changes in host cell gene expression near infected areas.